3HST

N-Terminal RNASE H domain of rv2228c from mycobacterium tuberculosis as a fusion protein with maltose binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.

Watkins, H.A.Baker, E.N.

(2010) J.Bacteriol. 192: 2878-2886

  • DOI: 10.1128/JB.01615-09

  • PubMed Abstract: 
  • The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryo ...

    The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase (CobC). The N-terminal domain of Rv2228c (Rv2228c/N) and the full-length protein were expressed as fusions with maltose binding protein (MBP). Rv2228c/N was shown to have RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein was shown to have additional CobC activity. The crystal structure of the MBP-Rv2228c/N fusion protein was solved by molecular replacement and refined at 2.25-A resolution (R = 0.182; R(free) = 0.238). The protein is monomeric in solution but associates in the crystal to form a dimer. The Rv2228c/N domain has the classic RNase H fold and catalytic machinery but lacks several surface features that play important roles in the cleavage of RNA/DNA hybrids by other RNases H. The absence of either the basic protrusion of some RNases H or the hybrid binding domain of others appears to be compensated by the C-terminal CobC domain in full-length Rv2228c. The double-stranded-RNase activity of Rv2228c/N contrasts with classical RNases H and is attributed to the absence in Rv2228c/N of a key phosphate binding pocket.


    Organizational Affiliation

    Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, 3A Symonds Street, Private Bag 92019, Auckland, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein
A, C
387Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein Rv2228c/MT2287
B, D
141Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Find proteins for P9WLH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WLH5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLR
Query on MLR

Download SDF File 
Download CCD File 
A, C
MALTOTRIOSE
AMYLOTRIOSE
C18 H32 O16
FYGDTMLNYKFZSV-PXXRMHSHSA-N
 Ligand Interaction
TAR
Query on TAR

Download SDF File 
Download CCD File 
C
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.632α = 90.00
b = 101.383β = 109.01
c = 76.091γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Refinement description